RetrogeneDB ID: retro_ecab_179

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 1:104002470..104002992(-)
• Located in intron of: ENSECAG00000017976

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SPRYD7
• Ensembl ID: ENSECAG00000011472
• Aliases: None
• Description: SPRY domain containing 7 [Source:HGNC Symbol;Acc:14297]

Sequence

>retro_ecab_179
AAGGAGATGCCGGCCATGCAGCTGGATACGCAGCACATGGGAGCAGATGTTGTCATTGTGAAAAATGGGAGAAGAATATG
TGGAACAGGAGGTTGTTTAGCCAGTGTGCCTTTACATCAAAACAAAAGCTACTTTGAATTCAAAATCCAGTCCACAGGAA
TCTGGGGTATTGGCGTTGCAACTCAGAAAGTTAACTTGAATCAGATTCCTCTTGGCCAAGATGTGCACAGTCTGGTGATG
AGAAATGATGGGGCCCTGTACCACAACAACGAGGAGAAAAATAGGCTGCCAGCAAACAGCCTTCCACAGGAGGGAGACCT
AGTGGGTATTACATATGACCAGGTAGAATTAAATGTGTATTTGAATGGAAAAAACATGCCTTGTCCAGCATCAGGCATAC
GAGGGACAATGTATCCAGTTGTTTATGTTGATGACAGTGCAATTTTGGATTGCCAGTTCAGTGAATTTTATCATATTCCT
CCGCCTGGTTTTGAAAAAATATCATTTGAACAGCAAATCTTC

Alignment

ORF - retro_ecab_179 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.95 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  REMPAVQLDTQHIGTDVVIVKNGRRICGTGGCLASAPLHQNKSYFEFKIQSTGIWGVGVATQKVNLNQIP
          .EMPA.QLDTQH.G.DVVIVKNGRRICGTGGCLAS.PLHQNKSYFEFKIQSTGIWG.GVATQKVNLNQIP
Retrocopy KEMPAMQLDTQHMGADVVIVKNGRRICGTGGCLASVPLHQNKSYFEFKIQSTGIWGIGVATQKVNLNQIP

Parental  LGRDVHSLVMRNDGALYHNNEEKNRLPANSLPQEGDVVGITYDHVELNVYLNGKNMHCPASGVRGTVYPV
          LG.DVHSLVMRNDGALYHNNEEKNRLPANSLPQEGD.VGITYD.VELNVYLNGKNM.CPASG.RGT.YPV
Retrocopy LGQDVHSLVMRNDGALYHNNEEKNRLPANSLPQEGDLVGITYDQVELNVYLNGKNMPCPASGIRGTMYPV

Parental  VYVDDSAILDCQFSEFYHTPPPGFEKILFEQQIF
          VYVDDSAILDCQFSEFYH.PPPGFEKI.FEQQIF
Retrocopy VYVDDSAILDCQFSEFYHIPPPGFEKISFEQQIF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP021940_articular_cartilage	0.12 RPM	2.30 RPM
SRP021940_cerebellum	0.62 RPM	9.76 RPM
SRP021940_embryo	0.20 RPM	4.04 RPM
SRP021940_placental_villous	1.11 RPM	6.59 RPM
SRP021940_synovial_membrane	0.30 RPM	2.55 RPM
SRP021940_testis	0.58 RPM	7.03 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_179 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_179 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_179 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000011472	1 retrocopy	retro_ecab_179 ,
Monodelphis domestica	ENSMODG00000010799	2 retrocopies	retro_mdom_1497, retro_mdom_613,